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- EMDB-19407: Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound... -
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Open data
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Basic information
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Title | Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24 | |||||||||
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![]() | E3 ligase / Complex / LIGASE | |||||||||
Function / homology | ![]() regulation of natural killer cell activation / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding ...regulation of natural killer cell activation / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / immune system process / negative regulation of reproductive process / negative regulation of developmental process / small molecule binding / cullin family protein binding / viral release from host cell / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of viral genome replication / positive regulation of gluconeogenesis / regulation of circadian rhythm / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / rhythmic process / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / chromosome, telomeric region / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / protein ubiquitination / DNA repair / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Shilliday F / Lucas SCC / Richter M / Michaelides IN / Fusani L | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Optimization of Potent Ligands for the E3 Ligase DCAF15 and Evaluation of Their Use in Heterobifunctional Degraders. Authors: Simon C C Lucas / Afshan Ahmed / S Neha Ashraf / Argyrides Argyrou / Matthias R Bauer / Gian Marco De Donatis / Sylvain Demanze / Frederik Eisele / Lucia Fusani / Andreas Hock / Ganesh ...Authors: Simon C C Lucas / Afshan Ahmed / S Neha Ashraf / Argyrides Argyrou / Matthias R Bauer / Gian Marco De Donatis / Sylvain Demanze / Frederik Eisele / Lucia Fusani / Andreas Hock / Ganesh Kadamur / Shuyou Li / Abigail Macmillan-Jones / Iacovos N Michaelides / Christopher Phillips / Marie Rehnström / Magdalena Richter / Monica C Rodrigo-Brenni / Fiona Shilliday / Peng Wang / R Ian Storer / ![]() ![]() ![]() Abstract: Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ...Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ligases could limit the potential of their application. To address this, potent ligands for DCAF15 were optimized using cryo-EM supported, structure-based design to improve on micromolar starting points. A potent binder, compound , was identified and subsequently conjugated into PROTACs against multiple targets. Following attempts on degrading a number of proteins using DCAF15 recruiting PROTACs, only degradation of BRD4 was observed. Deconvolution of the mechanism of action showed that this degradation was not mediated by DCAF15, thereby highlighting both the challenges faced when trying to expand the toolbox of validated E3 ligase ligands for use in PROTAC degraders and the pitfalls of using BRD4 as a model substrate. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 51.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
Images | ![]() | 41.8 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8royMC ![]() 8roxC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.645 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_19407_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19407_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound t...
Entire | Name: Complex of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24 |
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Components |
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-Supramolecule #1: Complex of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound t...
Supramolecule | Name: Complex of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: DDB1- and CUL4-associated factor 15
Macromolecule | Name: DDB1- and CUL4-associated factor 15 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 66.822609 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMAPSSKS ERNSGAGSGG GGPGGAGGKR AAGRRREHVL KQLERVKISG QLSPRLFRKL PPRVCVSLKN IVDEDFLYAG HIFLGFSKC GRYVLSYTSS SGDDDFSFYI YHLYWWEFNV HSKLKLVRQV RLFQDEEIYS DLYLTVCEWP SDASKVIVFG F NTRSANGM ...String: GSHMAPSSKS ERNSGAGSGG GGPGGAGGKR AAGRRREHVL KQLERVKISG QLSPRLFRKL PPRVCVSLKN IVDEDFLYAG HIFLGFSKC GRYVLSYTSS SGDDDFSFYI YHLYWWEFNV HSKLKLVRQV RLFQDEEIYS DLYLTVCEWP SDASKVIVFG F NTRSANGM LMNMMMMSDE NHRDIYVSTV AVPPPGRCAA CQDASRAHPG DPNAQCLRHG FMLHTKYQVV YPFPTFQPAF QL KKDQVVL LNTSYSLVAC AVSVHSAGDR SFCQILYDHS TCPLAPASPP EPQSPELPPA LPSFCPEAAP ARSSGSPEPS PAI AKAKEF VADIFRRAKE AKGGVPEEAR PALCPGPSGS RCRAHSEPLA LCGETAPRDS PPASEAPASE PGYVNYTKLY YVLE SGEGT EPEDELEDDK ISLPFVVTDL RGRNLRPMRE RTAVQGQYLT VEQLTLDFEY VINEVIRHDA TWGHQFCSFS DYDIV ILEV CPETNQVLIN IGLLLLAFPS PTEEGQLRPK TYHTSLKVAW DLNTGIFETV SVGDLTEVKG QTSGSVWSSY RKSCVD MVM KWLVPESSGR YVNRMTNEAL HKGCSLKVLA DSERYTWIVL UniProtKB: DDB1- and CUL4-associated factor 15 |
-Macromolecule #2: DNA damage-binding protein 1
Macromolecule | Name: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 93.347078 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK ...String: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRNGIGG NGNS GEIQK LHIRTVPLYE SPRKICYQEV SQCFGVLSSR IEVQDTSGGT TALRPSASTQ ALSSSVSSSK LFSSSTAPHE TSFGE EVEV HNLLIIDQHT FEVLHAHQFL QNEYALSLVS CKLGKDPNTY FIVGTAMVYP EEAEPKQGRI VVFQYSDGKL QTVAEK EVK GAVYSMVEFN GKLLASINST VRLYEWTTEK ELRTECNHYN NIMALYLKTK GDFILVGDLM RSVLLLAYKP MEGNFEE IA RDFNPNWMSA VEILDDDNFL GAENAFNLFV CQKDSAATTD EERQHLQEVG LFHLGEFVNV FCHGSLVMQN LGETSTPT Q GSVLFGTVNG MIGLVTSLSE SWYNLLLDMQ NRLNKVIKSV GKIEHSFWRS FHTERKTEPA TGFIDGDLIE SFLDISRPK MQEVVANLQY DDGSGMKREA TADDLIKVVE ELTRIH UniProtKB: DNA damage-binding protein 1, DNA damage-binding protein 1 |
-Macromolecule #3: DET1- and DDB1-associated protein 1
Macromolecule | Name: DET1- and DDB1-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.855297 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADFLKGLPV YNKSNFSRFH ADSVCKASNR RPSVYLPTRE YPSEQIIVTE KTNILLRYLH QQWDKKNAAK KRDQEQVELE GESSAPPRK VARTDSPDMH EDT UniProtKB: DET1- and DDB1-associated protein 1 |
-Macromolecule #4: 1-[5-[[3,4-bis(chloranyl)-1~{H}-indol-7-yl]sulfamoyl]-3-methyl-fu...
Macromolecule | Name: 1-[5-[[3,4-bis(chloranyl)-1~{H}-indol-7-yl]sulfamoyl]-3-methyl-furan-2-yl]carbonyl-~{N}-methyl-piperidine-4-carboxamide type: ligand / ID: 4 / Number of copies: 1 / Formula: A1H18 |
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Molecular weight | Theoretical: 513.394 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 405189 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |